+Open data
-Basic information
Entry | Database: PDB / ID: 1aus | ||||||
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Title | ACTIVATED UNLIGANDED SPINACH RUBISCO | ||||||
Components | (RIBULOSE BISPHOSPHATE CARBOXYLASE/OXYGENASE) x 2 | ||||||
Keywords | LYASE (CARBON-CARBON) | ||||||
Function / homology | Function and homology information photorespiration / ribulose-bisphosphate carboxylase / ribulose-bisphosphate carboxylase activity / reductive pentose-phosphate cycle / monooxygenase activity / chloroplast / magnesium ion binding Similarity search - Function | ||||||
Biological species | Spinacia oleracea (spinach) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.2 Å | ||||||
Authors | Taylor, T.C. / Andersson, I. | ||||||
Citation | Journal: Biochemistry / Year: 1997 Title: Structure of a product complex of spinach ribulose-1,5-bisphosphate carboxylase/oxygenase. Authors: Taylor, T.C. / Andersson, I. #1: Journal: J.Mol.Biol. / Year: 1990 Title: Crystallographic Analysis of Ribulose 1,5-Bisphosphate Carboxylase from Spinach at 2.4 Angstroms Resolution Authors: Knight, S. / Andersson, I. / Branden, C.-I. #2: Journal: Science / Year: 1989 Title: Reexamination of the Three-Dimensional Structure of the Small Subunit of Ru(Dot)Bis(Dot)Co from Higher Plants Authors: Knight, S. / Andersson, I. / Branden, C.-I. #3: Journal: Nature / Year: 1989 Title: Crystal Structure of the Active Site of Ribulose-Bisphosphate Carboxylase Authors: Andersson, I. / Knight, S. / Schneider, G. / Lindqvist, Y. / Lundqvist, T. / Branden, C.-I. / Lorimer, G.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1aus.cif.gz | 434.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1aus.ent.gz | 367 KB | Display | PDB format |
PDBx/mmJSON format | 1aus.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1aus_validation.pdf.gz | 507.6 KB | Display | wwPDB validaton report |
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Full document | 1aus_full_validation.pdf.gz | 548.1 KB | Display | |
Data in XML | 1aus_validation.xml.gz | 79.3 KB | Display | |
Data in CIF | 1aus_validation.cif.gz | 109.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/au/1aus ftp://data.pdbj.org/pub/pdb/validation_reports/au/1aus | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Atom site foot note | 1: CIS PROLINE - PRO L 176 | ||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS oper:
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Details | MTRIX THE TRANSFORMATIONS PRESENTED ON MTRIX RECORDS BELOW DESCRIBE NON-CRYSTALLOGRAPHIC RELATIONSHIPS AMONG THE VARIOUS DOMAINS IN THIS ENTRY. APPLYING THE APPROPRIATE MTRIX TRANSFORMATION TO THE RESIDUES LISTED FIRST WILL YIELD APPROXIMATE COORDINATES FOR THE RESIDUES LISTED SECOND. APPLIED TO TRANSFORMED TO MTRIX RESIDUES RESIDUES RMSD M1 L 20 .. L 463 ? 20 .. ? 463 M1 S 1 .. S 123 ? 1 .. ? 123 M2 L 20 .. L 463 ? 20 .. ? 463 M2 S 1 .. S 123 ? 1 .. ? 123 M3 L 20 .. L 463 ? 20 .. ? 463 M3 S 1 .. S 123 ? 1 .. ? 123 THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT CONTAINS FOUR LARGE AND FOUR SMALL SUBUNITS RELATED BY A FOUR-FOLD AXIS THROUGH THE MOLECULAR CENTER AT X=0, Y=1/4, Z=1/4. THE TRANSFORMATIONS GIVEN IN THE *MTRIX* RECORDS BELOW WILL GENERATE AN L4S4 HALF-MOLECULE FROM THE COORDINATES IN ENTRY. TO GENERATE THE FULL L8S8 MOLECULE FROM L4S4 THE FOLLOWING TWO-FOLD ROTATION ABOUT THE CRYSTALLOGRAPHIC TWO-FOLD AXIS ALONG Y HAS TO BE APPLIED: SYMMETRY1 1 -1.000000 0.000000 0.000000 0.00000 SYMMETRY2 1 0.000000 1.000000 0.000000 0.00000 SYMMETRY3 1 0.000000 0.000000 -1.000000 101.50000 |
-Components
#1: Protein | Mass: 52734.680 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / Organ: LEAF References: UniProt: P00875, ribulose-bisphosphate carboxylase #2: Protein | Mass: 14638.671 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / Organ: LEAF References: UniProt: Q43832, ribulose-bisphosphate carboxylase #3: Chemical | ChemComp-MG / #4: Chemical | ChemComp-FMT / #5: Water | ChemComp-HOH / | Compound details | RESIDUE L 201 IS A MODIFIED ACTIVATOR LYSINE WHICH IS CARBAMYLATED AT THE EPSILON-AMINO GROUP. THE ...RESIDUE L 201 IS A MODIFIED ACTIVATOR LYSINE WHICH IS CARBAMYLAT | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.35 Å3/Da / Density % sol: 47.68 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS Temperature: 4 ℃ / Method: vapor diffusion, hanging drop / Details: Taylor, T.C., (1996) Nat. Struct. Biol., 3, 95. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87 |
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Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 28, 1994 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.87 Å / Relative weight: 1 |
Reflection | Resolution: 2→20 Å / Num. obs: 130977 / % possible obs: 89 % / Observed criterion σ(I): 2 / Redundancy: 6 % / Rmerge(I) obs: 0.105 |
Reflection | *PLUS Highest resolution: 2.2 Å / Lowest resolution: 20 Å / Num. obs: 107965 / % possible obs: 85 % / Num. measured all: 799161 / Rmerge(I) obs: 0.103 |
-Processing
Software |
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Refinement | Resolution: 2.2→7 Å / σ(F): 2
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Displacement parameters | Biso mean: 16.01 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.27 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→7 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.207 / Rfactor Rfree: 0.224 / Rfactor Rwork: 0.207 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 16.019 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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